diff --git a/README.md b/README.md index ec59bb32..c4216b58 100755 --- a/README.md +++ b/README.md @@ -9,8 +9,8 @@ The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for functional annotation and translation of individual tumor genomes for precision cancer medicine. It interprets primarily somatic SNVs/InDels and copy number aberrations, and has additional support for interpretation of bulk RNA-seq expression data. The software classifies variants both with respect to _oncogenicity_, and _actionability_. Interactive HTML output reports allow the user to interrogate the clinical impact of the molecular findings in an individual tumor. - Variant classification - - according to *oncogenicity*: evaluating the oncogenic potential of somatic DNA aberrations (VICC/CGC/ClinGen guidelines) - - according to *actionability*: mapping the therapeutic, diagnostic, and prognostic implications of somatic DNA aberrations (AMP/ASCO/CAP guidelines) + - according to *oncogenicity*: evaluating the oncogenic potential of somatic DNA aberrations ([VICC/CGC/ClinGen guidelines](https://pubmed.ncbi.nlm.nih.gov/35101336/)) + - according to *actionability*: mapping the therapeutic, diagnostic, and prognostic implications of somatic DNA aberrations ([AMP/ASCO/CAP guidelines](https://pubmed.ncbi.nlm.nih.gov/27993330/)) - Tumor mutational burden (TMB) estimation - Mutational signature analysis - Microsatellite instability (MSI) classification diff --git a/pcgrr/pkgdown/index.md b/pcgrr/pkgdown/index.md index 7dd81d2f..b4dfc897 100644 --- a/pcgrr/pkgdown/index.md +++ b/pcgrr/pkgdown/index.md @@ -10,8 +10,8 @@ editor_options: The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for functional annotation and translation of individual tumor genomes for precision cancer medicine. It interprets primarily somatic SNVs/InDels and copy number aberrations, and has additional support for interpretation of bulk RNA-seq expression data. The software classifies variants both with respect to _oncogenicity_, and _actionability_. Interactive HTML output reports allow the user to interrogate the clinical impact of the molecular findings in an individual tumor. - Variant classification - - according to *oncogenicity*: evaluating the oncogenic potential of somatic DNA aberrations (VICC/CGC/ClinGen guidelines) - - according to *actionability*: mapping the therapeutic, diagnostic, and prognostic implications of somatic DNA aberrations (AMP/ASCO/CAP guidelines) + - according to *oncogenicity*: evaluating the oncogenic potential of somatic DNA aberrations ([VICC/CGC/ClinGen guidelines](https://pubmed.ncbi.nlm.nih.gov/35101336/)) + - according to *actionability*: mapping the therapeutic, diagnostic, and prognostic implications of somatic DNA aberrations ([AMP/ASCO/CAP guidelines](https://pubmed.ncbi.nlm.nih.gov/27993330/)) - Tumor mutational burden (TMB) estimation - Mutational signature analysis - Microsatellite instability (MSI) classification